Sherlock Holmes, What Have You Done
by crystaljoygmagic
Summary: "Since when did I become Mr. Holmes to you?" Something was off. Something was very off about his pathologist. Post TRF
1. Chapter 1

I don't own the wonder that is Sherlock.

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She was like that with everyone. Moll- Dr. Hooper was acting perfectly unlike herself, void of any feelings.

Sure she talked to other staff members, but something wasn't right. For instance, Sherlock saw Mike Stamford starting to converse with Molly Hooper while they were doing the autopsy, the usual of course. But what quickly became apparent and quite peculiar was that she refused to carry out any form of communication. Yes Molly was replying to how her weekend was. But tight lipped, she merely answered with yes and no to questions pertaining to anything but her work. "How was the weekend Molly? Did you go see the new-" "No, I didn't Mr. Stamford could you pass the report Mrs. Deened made this afternoon? Thank you, I'll just be working alone from here on out." Walking out the door with her report, Mike stood frozen in her room.

As nice as she was being, she kept dismissing people and her smile; it didn't take Sherlock Holmes to see how fake that turned out to be. "Well, someone work up on the wrong side of bed, for once huh Holmes?" Stamford stated making his way out from the morgue. _Nothing out of the ordinary, Stamford's right. _Sherlock continued on looking in the microscope.

_U-gh!_ She wanted to throw everything off the table; put duct tape on anyone who attempted to make any form of conversation, fling herself off the biggest roof… well she knows there are ways to still be alive if she ever did that now. But she felt her blood boiling, heart pumping faster than ever Sherlock Holmes had done in the past, with his measly fake compliments. She even was cranky towards Toby. Feeling mildly guilty about pushing Toby off her legs, she promised to go home and give him an extra heap full of his favourite beefy snacks. Walking off to get something to eat, she heard someone call her name. "It's Dr. Hooper," she muttered and turned with a nice, perfect, nothing-in-the-world-is-wrong smile. "Oh Mary, in need of something?" Mary halted to a stop in front of her friend, "Nothing, I could do with a big lunch and a giant helpful of ice-cream though, let's get going! And what's with you asking everyone to call you Dr. Hooper now eh?" Falling back Molly felt an oncoming headache come on, "No, actually I'm just coming back from lunch. So sorry, see you whenever."She trailed off. _Or never. Great now no lunch either. _Mary stared at Molly's back in surprise, _why has Molly been avoiding everyone these past few days_? She never says no, to anything! And right blatant lie about coming back from lunch, Stamford was just saying how Molly's long overdue for her break. _Maybe she's having a tough day, Sherlock was back in the morgue. _Pulling out her phone, Mary texted John:** Free for lunch? Sherlock-I mean Molly's just stated she'd rather be alone today.**

Grabbing something out of the café just downstairs, Molly made her way back to her workplace. _Fuck, he's still here. _

Seeing Sherlock out of the corner of her eye, she opened up her file and began writing about any findings. She went on peacefully for a good two minutes until from the corner of her eye she saw Sherlock staring at her. Normally, she'd ignore the odd behavior. No, normally she'd gush and stutter until she figured out he was probably in his mind palace. Today she couldn't be arsed with him.

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Sherlock wasn't staring. He was noticing. Something was off. Something was very off about his pathologist. Besides the very fact that she'd only said two words to him- he's been in with her since this morning- Molly had made no attempts at asking of how's he's been and whatnot._ Did you have lunch Sherlock, you've been working so hard Sherlock, want to grab a bit to eat Sherlock._ Usually, no always, it would always irritate him how she asked after him as though he was a child, or a man who would actually be interested_. _But after hearing Stamford's jab at Molly earlier on, then just getting a text from John asking what _he'd _done (**nothing out of the ordinary, thank you very much**), Sherlock decided it was worth his time to deduce what the matter could be with Dr. Molly Hooper.

Rubbing his temples, Sherlock let out a frustrated growl. Nothing. There's wasn't anything to go on because nothing had changed in Molly Hooper, at least anything that can be physically detected from afar. Clothing the usual, unfitted and just cleaned. Shoes, comfy and perfectly cat hair free. Eyes, tired but none more so than usual therefore no sign of lack of sleep that could've resulted from the night prior. _What else, what else_? Hair, perfectly kempt in the classic Molly ponytail.

_Hmmm, when did it become the classic Molly ponytail? _Standing up, he walked to her table.

She couldn't find it in herself to be bothered as she popped a raspberry in her mouth. But now, with him standing right in front of her, he was demanding attention. Molly looked up and saw Sherlock with clenched fists and while that might be a scary sight at first, his expression was one of a tight lipped fake-as-they-can get smile. "What is it, what do you need?" No stuttering, no blush on her cheeks, one would say Molly Hooper had finally moved on but if her behavior is equalized amongst her colleagues as well, Sherlock had to make another assumption. "Are you feeling alright, Molly? Any symptoms of nausea, headache, or fever?" Molly's smile faltering she squeaked out in a controlled voice, "First of all _Mr. Holmes, it's Doctor Hooper._ Not too hard to say, if it feels too long you're perfectly permitted to not say anything at all. And why on earth would I not be fine. Signs of nausea? Not particularly at the moment but I did once I saw your pleasant face this morning. Headache? You might be giving me one no, check that, make that a yes, I am getting a headache. And to your last inquiry, no fever. Done deducing then? Now, if that would be all please leave me be to do my work!"

"I-"

"Oh, this is about the food inside the office isn't it? My BLOODY apologies, how dare the smell of food get in the way of YOUR office." Throwing the raspberry box into the garbage Molly sat back on the chair, fuming. That was the last straw, Sherlock Holmes deducing her, and for what? Not asking him to lunch which he will promptly say no to anyway?!

Taking the rational approach, Sherlock decided to calmly inquire, "Moll-Dr. Hooper, since when did I become Mr. Holmes to you?" "I'm not your friend as you've clearly stated oh so many times in the past, you merely come in to do work, and you're barely accountable as a colleague. And don't give me the you're so important to me Molly crap. We both know that's not true." Sherlock had no idea now why Molly was acting like this. After all that has happened, can she still not observe how important she was to everyone, to him?

"So I think it's perfectly fine to call you Mr. Holmes."

Trying to focus on her work, Molly tapped furiously her foot so that Sherlock would take a hint and leave. But this is Sherlock Holmes, and if nothing is stated directly, then there is no hint to be taken. Continuing on, Sherlock asked carefully, "Did your cat die then Molly? Has Toby reached an untimely death?"

_"Get out." _

"I beg your pardon?" Sherlock was taken aback by Molly's seething- _seething- _tone.

Closing her eyes for a minute, Molly breathed, "Now. I'm tired Sherlock. I'm tired and I'm done. I'm in my 30s, have absolutely nothing going for me, my best friend isn't human, I look as though I'm a zombie on my best days, and I manage to mess up any plans of my dream future which should include happiness and friends, family, success... Wait, I don't need to be telling this to some random man-."

"Since when did I become rando-" Molly held up her hand, "Do let me finish, I don't need some man asking me how I am feeling because guess what Sherlock Holmes, I'm finally taking your advice into account. And I do say I thank you for it."

"And what might that be Molly?"

Fighting the urge to punch Sherlock in the face, she found her voice and whispered, "Its Dr. Hooper, and you were right. About sentiment. It truly is for fools. Thank you for letting me see the right of your ways."

Molly trying to sound stronger than she was feeling, cleared her throat, "I think I'm going to take the rest of the day off; clearly you need the space for individual work. I'll finish my report tomorrow."

For the first time, Sherlock had no time to react seeing how quickly Molly pretty much ran out the door. Fearing for the worst, Sherlock quickly dialed for John:** John, something has gone horribly wrong. I think I lost Molly.**

**What? Sherlock, how did you lose Molly in the morgue-**

**No John, I may have broken her.  
**

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So, wow um hello! I hope you enjoyed that. I'm a long time Sherlolly fan and this is my very first Sherlock fic so hopefully it's not too bad. I wish I took more time to edit but I was very excited to show Molly in ...an angry way and see how Sherlock would respond to that. I'm not sure if this will be left as a one-shot or multi-chapter just yet, do let me know what you think. Once again, thank you thank you thank you for just reading it and my apologies for anything that might be out of the ordinary (specifically the conversations because I'm not British, so it was tough trying to not sound Canadian haha).

Also, I am on tumblr so ask for it if you'd like :D


	2. Chapter 2

First of all, thank you times a BILLION for the lovely lovely comments and favourites. Truly, the sherlock fandom has the most wonderful and open fans ever and I'm so proud to be one (no matter what anyone else says)!

PondCreature, Rocking the Redhead, Renaissancebooklover108, crooney83, SammyKatz, and Reina434, you guys truly made my week with the most encouraging comments!

And thank you for the suggestions also, I've done my best to keep spelling and grammar at best ( I don' have a beta so I've just triple checked things). Anyhoo, have a lovely time reading it (actually it's not a very fun read, this chapter).

I don't own the wonder that is Sherlock.

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It was exactly eight days ago that Sherlock had last gone to the morgue. The previous case was solved already and he was still awaiting a new one. No wait, John kept insisting the case of poisoned children is at least a seven. "How on earth is it a seven, John? Can't you see it was the babysitter doing it? It was the same one for the other four murders, how on earth could it have been the parents! Hardly even a three, I'm surprised at how even Anderson couldn't have figured this one out."

John rolled his eyes, the constant bickering was fairly normal and he's finally figured out Sherlock- surprisingly- means no hurt when he states everything – quite literally, everything. "Alright then, I don't know why you won't make exceptions for cases under a six when obviously you haven't gotten any good ones for a while. It'll do more good than harm, and I mean that for poor Mrs. Hudson downstairs. She needs her sleep, Sherlock and you playing that bloody violin for eight nights straight isn't exactly helping.

The couch was clearly becoming too small for Sherlock's presence, especially when John can see the impatience running through his whole body, clear signs of twitching and mopping about. "I already have a case John. One I might consider one of the most important ones in the past few months."

John's eyebrows rose a bit, "Oh and you didn't care to mention that? Off to solve the best ones yourself then?"

"No."

"Ok, so is this because I was out with Mary last week? Keep in mind I do have to spend some tim-" "It's NOT that John, its Molly. I remember distinctly telling you she's been acting up recently. I was in the morgue last week and she was talking so … indifferently with everyone; Mary, Mike, those student pathologists. Something's wrong, she's met someone bad, probably a criminal. Can't you see Molly will lead us to a case that will no doubt get you many hits on your _blog!" _John was gaping at Sherlock. He didn't know where to start; rage, shock, even curiosity.

"Ok, first of all, Sherlock…" John pointed a finger to his lips trying to keep the colorful words at bay, "You want to know what's wrong with Molly. I gathered as much from your call last week, but did you think for one second that oh I dunno, to FEEL a bit more! Stop treating her like one of your cases. Worse, you've just stated you want to use Molly to get a good case. Maybe, maybe you can try solving it because you genuinely worry for her well being. Second of all, I DON'T put everything on the blog!"

Sherlock was perplexed; his flat mate can be so daft sometimes. "What? Is that what you think? Of course I want to help her, my treating this as a case will obviously help. If I treat it rationally I can solve it much faster. Besides, I didn't find it the least bit amusing how she treated me as complete stranger." Sherlock muttered the last bit under his breath.

"Good, so we've established that you are in fact human and you do actually care about Molly Hooper. Good, yes, excellent. We are finally getting somewhere with that emotional side of yours." John broke off at Sherlock rolling his eyes. _Almost forgot I'm dealing with a 15 year old._

"Alright then, if that's settled and you best keep in mind that HELPING Molly is the priority, then why don't I give her a call? We'll have her over and chat and-" John once again paused when he heard Sherlock mutter _stupid._

Part glaring, John questioned, "Alright then, what's wrong with my plan, Mr. Social Butterfly?"

"I've clearly not gone to the morgue, no John not because I don't have a case but because I was giving time to Molly. She was unhappy with me primarily, stated by how she couldn't bottle anything in with her having a shout at me. Now, if it's a temporary anger it would've died out in a few days, at most five. But, your girlfriend is worried about Molly because she keeps refusing to even talk to anyone for a mere five minutes without running out, and 'looking more miserable than ever'." John, fighting the rage to tell Sherlock to quit peeking at his texts, allowed Sherlock to continue with a dramatic wave of his hand. "The plan now is that tomorrow I shall be at the morgue, by myself of course being the fine specimen that I am and try to make her lash out at me."

"Um."

"Yes?"

"How is that any different from my plan Sherlock? I mean the results, my way is much nicer and Molly will probably not hate you as much by the end of it."

Rubbing his hair into all sorts of directions, Sherlock let out a frustrated groan saying, "John please, Molly will hide more than ever before that anything is wrong if we try to _coax _her into saying it. It's much more efficient to go with my plan. She'll shout out everything that's on her mind. She's not one to hide things, till now. As for her hating me…" Sherlock broke off.

_Well, I don't want her to hate me. But she won't, this is Molly and I'm Sherlock. We're…we can't stay mad at each other. Especially Molly, no she can't hate me._

_"_Her hate towards me won't last. It's Molly."

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"I'm not leaving you till you tell me what's wrong! Enough is enough and I'll follow you to your place if I must." Mary is done with Molly's attitude. At first she left her to be, assuming it was a one-off. But after a few days and a few worrisome questions, Molly still wouldn't reply except with a quiet 'just fine'. Finding her walking glumly, Mary took advantage of Molly's weak situation and pushed her into the confines of a place with only a timed exit.

Pushing the elevator button for the ground floor, Molly tried to keep herself together. "Mary, I love you and I'm eternally grateful for caring about me," -_at least one person cared if I suddenly decide to drop out of the face of the planet, _Molly decided to leave that bit out, "but I really am fine. I've just been really busy at the morgue, there's a lot more bodies coming in these few weeks."

Exasperated, Mary calmly persuaded, "Molly please, you're probably the only one in the world who looks forward to an extra body or two. Well, besides Sherlock." At the mention of the name, Molly couldn't help but glance down at her feet, looking more and more like she was suffering from a wound. "Oh dear, what has he done now? You know you shouldn't even take him seriously or let him in your morgue, what with the way he always treats you. And him being John's friend is no excuse."

Molly's head whipped up and started shaking her head at the accusation. "Sherlock hasn't done a thing," Molly's entire tone was accusatory however. _No, Sherlock has done nothing. As always. Nothing at all, this would be a problem to a Molly who cared. But not any longer._

_I'm done with caring. Why are people suddenly caring about me now that I've given up on life?_

With no place to escape in the tine elevator, Molly replied,"It's just…I'm sick and tired of hoping Mary. People don't realize, but when you've had nothing going for you for _years _it's so much harder trying to be optimistic about life. I'm just….I'm done with hoping things will turn out well for me." Biting her lip and letting out a nervous and bitter laugh, Molly exclaimed, "I'm sorry, Mary. I never meant to hurt you and it's not anyone's fault. But from now on, I'm just going to live my life with a more…realistic perspective rather than an optimistic fool." _Like a machine. _ Yelling a goodbye, Molly began exiting the elevator as soon as the doors opened, without looking at her friend's expressions.

Mary will pull out her phone to call John as soon as the shock wears off.

**John. **

**Yes, m'dear. Coming ove-**

**This is serious, John. There's something very wrong with Molly. **

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That wasn't a very happy read was it? I tried to keep the John and Sherlock banter a little silly for lightness, but once again my apologies, but I just want to say 1) sorry for the long wait and anything irritating with the story (do let me know) 2) most of the story probably won't be the most cheerful of reads, and 3) THANK YOU again for putting a smile on my face with the wonderful comments :D. Let me know again what you thought of this chapter if it won't be much trouble!


	3. Chapter 3

Gah! Has it been this long already?! Now, I know why it takes so long to update for authors. You look at the time and it's suddenly been months! No but really guys, SINCEREST apologies. I know how annoying it can be to be waiting for a story to update, my only excuse would be university :( BUT I promised myself this weekend that I would update this fic today before midterms started up again and here we are. Not exactly Molly-centric, but she's still mentioned and concerns for her are still going up. Like I've said, I know where this story is going but I'm not too sure how many chapters it would take to get everything out (if you guys have a preference do let me know if you prefer this story to be under or over 7ish chapters).

Also, shortie linking chappie.

I don't own the wonder that is Sherlock.

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Sherlock Holmes is not patient, whatsoever. No, most who knew him would certainly say he is in fact, quite the opposite. At this moment, John Watson was watching Sherlock test the quality of milk-_milk- _at the St. Barts Morgue not knowing how to go about talking with his friend. He'd run out of specimens to test and was now tapping his fingers, waiting with an irritating twitch in his left eyebrow.

Letting out a cough to break the silence, he started, "So, you're sure she was to come in today? I mean, she could've switched shifts with that new pathologist right?"

"Hm. Of course, I know her schedule."

John let out a loud sigh. The two men had been waiting for over an hour and a half to confront Molly about her…newfound perspective on life. After Mary filled John (and thereby Sherlock) in on what happened in the elevator, John saw that Sherlock was more and less just confused by her sudden behavior. He knew Sherlock would act out more harshly to the pathologist because of the built up frustration and so decided that he would 'supervise' their confrontation. After all, Molly did indeed became a close friend of his after Sherlock's return and owed her at least a censored Sherlock after all she'd done to save his life from the Moriarty problem.

"_Why on earth should it matter now? After all this time of remaining ordinarily the same, why is she upset now?!" _Sherlock had been muttering to himself, but John heard him over the microscope. John knew this was the beginning of a rant coming on and was about to prepare himself to give Sherlock another lesson of what is and what's not good in a social context when Mike came in with the morgue keys in hand. "Oh sorry, I didn't know anyone was in, thought that new pathologist left hours ago. I'm afraid your experiments will have to be postponed for the night Sherlock, gots to lock up," Mike jiggled the keys to get Sherlock's attention from the microscope.

"Oh, so was Molly not scheduled in for today?" John asked rather smugly, looking at Sherlock. The man thought himself to be too brilliant and sometimes, getting things wrong (ergo bruising that gigantic ego) would do him some good. "No she was mate, but she never showed. She usually calls in whenever she can't come in, so I called her just to check if she was doing alright during my break."

Sherlock was putting his coat on all the while storing the information from Mike and with a wave of his hand, urged him to continue. "I called her mobile and she said it slipped her mind to call and her phone was dying so I couldn't talk too long." "Why her mobile?" Sherlock interrupted, "Do co-workers not try home phones before secondary numbers?" "It went to voicemail when I tried her landline first. And when I was talking to her it didn't sound like she was home, heard lots of background voices and music blaring I think."

_Who goes to parties or clubs in the middle of the day? _Sherlock could see John contemplating the same question.

With that, Sherlock took off with John close behind. Reaching for his phone, he told John to call a cab while he tried to get a hold of Molly. Trying another time after his first call went to voicemail; he got in the cab knowing John was waiting for an explanation for where they were off to. "We're going to Molly's to see whether or not she's back yet. Molly would never skip work unless she had a legitimate reason, her recent personal opinion of living her life has taken a drastic change and now she's getting careless? It's as though she's taking on an entire new persona! Hello? Molly?!" Sherlock let out a deep breath when he heard her voice. He didn't comprehend why he was so worried, but this Molly Hooper had become too unpredictable for Sherlock Holmes to know where- or how she's been. John waited outside the cab while Sherlock jumped out of the cab to see if Molly was home.

"Molly, where are you? We need to talk. Are you home? I'm about to come up to your flat in approximately fifty-five seconds." Sherlock waited for a response but all he heard were some distant music and Molly's occasional squeals. "Molly, can you hear me? I need-"

**The line went dead.**

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I'd like to thank fanficnerd700, happywhale15, Green String , louvreangel, SammyKatz, SpencerReidFan89 , Anatomydoc, Lalalupin , yay, crooney83 ,Renaissancebooklover108 for putting a smile on my face!

So not a lot of Sherlock-Molly communication here, it will happen soon! But fear not, Sherlock is not one to give up easily, especially on Molly.

Next update: I'm not going to say when, probably as soon as university work-load dies down and/or a spur of the moment midnight writing mayhem. BUT I can promise you that it WILL be completed before Sherlock Season 3 ( and if that happens to come out next month,then well I guess I am willing to drop outta uni then haha!)


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